Former Mets clubhouse manager Charlie Samuels pleaded not guilty yesterday in Queens Criminal Court to charges that he systemically looted some $2.3 million worth of collectibles, including jerseys, bats, helmets and other equipment — much of it signed.

“The autographed sports memorabilia and collectibles industry has become a multibillion-dollar industry, and this case exposes its darker side — the enthusiast who does not collect for personal enjoyment but rather stockpiles hundreds of pieces of sports memorabilia as a long-term investment,” said Queens District Attorney Richard Brown.

Samuels, 53, who spent almost his entire adult life working for the Mets, was also accused of falsifying business records so he could skim $25,000 off meal money the Mets provide to umpires, and of cheating on his city and state taxes to save $24,000 over two years by not declaring the tips players gave him.

“The defendant had a dream job that any Mets fan would die for, and he blew it,” Brown said.

Samuels was released on $75,000 cash bail, but faces between 8 1/3 and 25 years in prison if convicted.

His defense attorney, Michael Bachner, said, “Charlie was entitled to the unsigned property, and over time had players sign it . . . It was throwaway material.

“After reviewing the indictment, we are shocked at the nature of these accusations. The indictment barely made it to first base.”

Samuels started working for the Mets in 1976. He was made equipment manager in 1983 and later became clubhouse manager and traveling secretary.

He is accused of stealing 507 jerseys, 828 bats, 304 hats, 22 batting helmets and 10 equipment bags that were found in a friend’s basement in Madison, Conn.

The Mets fired him last year after an audit found he wrote checks from the team to cover his personal expenses.

“The Mets terminated Charlie Samuels’ employment with the organization on November 12, 2010, following an internal investigation in which we discovered improprieties and violations of club policies,” the team said in a written statement.